ASAPCGIDisplay.cgi error - OMSSA and iProphet .prot.xml

[dctrud]

I'm encountering a problem with ASAPCGIDisplay.cgi giving the message
"error" and not displaying any information when I click on a protein
level ratio in the .prot.xml viewer. This is occurring for OMSSA and
iProphet results only. X!Tandem and Mascot results seem to work fine.
Ratios and p-values are calculated without problem, and display in
the .prot.xml viewer in all cases. It's only the ASAPCGIDisplay.cgi
stuff that's not working. Peptide level asapratio display with
ASAPRatioPeptideCGIDisplayParser.cgi is working okay in all cases.

I've had a look at the tags in files but can't see any obvious
problem. Am using the 4.3.1 release.

I've uploaded three files to the group file area which illustrate the
problem.

asap_iprophet_not_working.prot.xml
asap_omssa_not_working.prot.xml
asap_tandem_working.prot.xml

I'd be very grateful if someone familiar with the CGIs could have a
look.

Dave Trudgian

[Jake W]

Dave--

I encountered the same problem. I think you just need to add OMSSA to
the getSearchResult function. Try adding the following:

ASAPRatioProteinCGIDisplayParser.cxx, @ line 2030:
if(! strcasecmp(engine, "OMSSA"))
return new OMSSAResult(tags);

ASAPRatioProteinCGIDisplayParser.h, @ line 56:
#include "Parsers/Algorithm2XML/SearchResult/OMSSAResult.h"

Hope that helps,
Jake

[Dave Trudgian]

Jake, Thanks for this, the CGI works for OMSSA results now.

Looking at ASAPRatio info in the prot.xml viewer still fails for
iProphet merges from multiple search engines. Have you come across this
issue? I'm wondering if it's a bug, or just something not supported yet.

DT

--
Dr. David Trudgian
Bioinformatician in Proteomics
University of Oxford

Mon-Thu: CCMP, Roosevelt Drive
Tel: (+44) (01865 2)87784

Friday : Dunn School of Pathology, S. Parks Rd.
Tel: (+44) (01865 2)75557

[David Shteynberg]

Hi Dave,

This is not supported yet. Hopefully, this will become supported in
the near future. Please send anymore issues you find like this here.

Thanks,

-David